Hello FreeSurfer experts,
I recently downloaded and installed FreeSurfer on my Mac computer, but I
have a few questions about the startup.
1. When I run FreeSurfer, I get the following. I know the Wiki says to
ignore the warning, and FreeSurfer does run normally after this, but I
wanted to be sure it really was not a problem.
[SiriasBook:/] csirias% setenv FREESURFER_HOME Applications/freesurfer/
[SiriasBook:/] csirias% source Applications/freesurfer/SetUpFreeSurfer.csh
-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME Applications/freesurfer/
FSFAST_HOME Applications/freesurfer//fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR Applications/freesurfer//subjects
WARNING: The /Users/csirias/matlab/startup.m file does not appear to be
configured correctly. You may not be able
to run the FS-FAST programs
Try adding the following lines to /Users/csirias/matlab/startup.m
-----------------cut---------------------
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/matlab',fshome);
if (exist(fsmatlab) == 7)
path(path,fsmatlab);
end
clear fshome fsmatlab;
fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
if (exist(fsfasttoolbox) == 7)
path(path,fsfasttoolbox);
end
clear fsfasthome fsfasttoolbox;
-----------------cut---------------------
MNI_DIR Applications/freesurfer//mni
[SiriasBook:/] csirias%
2. When I type in 'freeview' to the command line, I get several other
messages as the program opens. I am not sure if they are a problem, but
here they are. I seem to be able to run freeview despite these messages,
but some others have told me that these messages do not appear on their
computers, so I am wondering why they appear.
[SiriasBook:/] csirias% freeview
2013-06-10 12:22:57.739 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.740 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.754 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.755 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.768 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.769 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.781 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.782 Freeview[1200:303] invalid drawable
3. And my last question. How do I run FreeSurfer automatically when I open
the terminal window? I would like to just type 'freeview' into the command
line to have the program run, but I currently have to type
setenv FREESURFER_HOME Applications/freesurfer/
followed by
source Applications/freesurfer/SetUpFreeSurfer.csh
in order for the program to run.
Thank you so much for any help you can give! Like I said, the program
appears to run normally despite the messages, but I just want to know why
they are appearing. The last question is more of a convenience issue.
Thanks,
David
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